12-94548447-T-C

Variant names:

• chr12-94548447-T-C
• rs7139313
• ENST00000307241.5:n.207T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000307241.5(SUCLG2P2):​n.207T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 1,595,280 control chromosomes in the GnomAD database, including 318,870 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.67 (34438 hom., cov: 33)
  • Exomes 𝑓: 0.62 (284432 hom.)
• Consequence: SUCLG2P2 ENST00000307241.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399
• Publications: 8 publications found

Genes affected

SUCLG2P2 (HGNC:43997): (SUCLG2 pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUCLG2P2		n.94548447T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUCLG2P2	ENST00000307241.5	n.207T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101412 AN: 151996 Hom.: 34383 Cov.: 33

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.666

GnomAD4 exome AF: 0.625 AC: 901583 AN: 1443166 Hom.: 284432 Cov.: 29 AF XY: 0.624 AC XY: 448502 AN XY: 719152

African (AFR) AF: 0.752 AC: 24823 AN: 33006

American (AMR) AF: 0.757 AC: 33855 AN: 44698

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 17801 AN: 26034

East Asian (EAS) AF: 0.890 AC: 35231 AN: 39606

South Asian (SAS) AF: 0.623 AC: 53467 AN: 85772

European-Finnish (FIN) AF: 0.617 AC: 32891 AN: 53280

Middle Eastern (MID) AF: 0.613 AC: 2522 AN: 4112

European-Non Finnish (NFE) AF: 0.604 AC: 662645 AN: 1097004

Other (OTH) AF: 0.643 AC: 38348 AN: 59654

GnomAD4 genome AF: 0.667 AC: 101530 AN: 152114 Hom.: 34438 Cov.: 33 AF XY: 0.669 AC XY: 49761 AN XY: 74350

African (AFR) AF: 0.753 AC: 31250 AN: 41512

American (AMR) AF: 0.707 AC: 10810 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2379 AN: 3468

East Asian (EAS) AF: 0.874 AC: 4524 AN: 5174

South Asian (SAS) AF: 0.640 AC: 3088 AN: 4822

European-Finnish (FIN) AF: 0.606 AC: 6401 AN: 10560

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41072 AN: 67976

Other (OTH) AF: 0.671 AC: 1413 AN: 2106

Alfa AF: 0.626 Hom.: 126463

Bravo AF: 0.679

Asia WGS AF: 0.783 AC: 2722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	1.3
DANN	Benign	0.32
PhyloP100		0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7139313; hg19: chr12-94942223;